puremoe

1.1.0

Integrated Retrieval and Analysis of 'PubMed', 'NIH', and 'NLM' Literature Data

0packages depend

3.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Jason TimmFirst published 2024-04-196 releasesCRAN page ↗GitHub ↗

Retrieve and analyze biomedical literature from 'PubMed' and the wider 'NIH'/'NLM' data stack through a single, PMID-centered interface. A PubMed search resolves to a set of PMIDs, which can be used to retrieve article metadata and abstracts, author affiliations, 'iCite' citation data and links, 'PubTator3' entity and relation annotations, and open-access full text from 'PMC'. A local analysis layer operates on the retrieved tables, supporting corpus expansion through citation links, citation network construction, sentence-level entity co-occurrence, inspection of relation evidence, and 'MeSH' descriptor keyness.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("puremoe", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("jaytimm/puremoe")

Development version from jaytimm/puremoe. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-puremoe

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-puremoe

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-puremoe

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.7 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.20

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-06-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-23
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-21
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 6 earlier snapshots

ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-28
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

3.6K

CRAN downloads in the past year

Rank #8,501 · ~10/day · ~300/mo

puremoe Releases R versions

Daily download trend is not available in this view yet.

52330 days

1.4K90 days

3.6K1 year

Compare downloads with other packages →

Also on117 r2u18 autocran

Repository

GitHub ↗ jaytimm/puremoe

4Stars

0Forks

2Open issues

0Open PRs

0Releases

pubmed-centralpubmed-parser

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (12)

rentrez textshape xml2 data.table httr pbapply jsonlite rappdirs textpressparalleltoolsutils

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown DT dplyr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 3,579 (83%)Rd 672 (16%)Vignettes 36 (1%)

Code characteristics

Cyclomatic complexity: 3.5 median / 26 max
Test cases: 38 / 0.20 per code line
Documented parameters: 99%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

54 13 exported

Complexity

6.1 avg / 26 max

Call network

54 nodes / 42 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Jason Timm

Author, Maintainer

Authors (1)

Jason Timm

Author, Maintainer

Release timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

1.1.0Latest
2026-06-24 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.4
2026-04-21 · diff ↗
1.0.3
2026-01-27 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.2
2024-10-15 · diff ↗
1.0.1
2024-05-13 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.0
2024-04-19
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-19
Total releases: 6 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Bundled data: 359 KB / 1 file
Download size: 24 KB
Installed size: not tracked yet
With dependencies: not tracked yet